MendelianViolationMetrics – GATK

Metrics

Overview

Describes the type and number of mendelian violations found within a Trio.

This table summarizes the values that are specific to this metric.

Metric	Summary
FAMILY_ID	The family ID assigned to the trio for which these metrics are calculated.
MOTHER	The ID of the mother within the trio.
FATHER	The ID of the father within the trio.
OFFSPRING	The ID of the offspring within the trio.
OFFSPRING_SEX	The sex of the offspring.
NUM_VARIANT_SITES	The number of biallelic, SNP sites at which all relevant samples exceeded the minimum genotype quality and depth and at least one of the samples was variant.
NUM_DIPLOID_DENOVO	The number of diploid sites at which a potential de-novo mutation was observed (i.e. both parents are hom-ref, offspring is not hom-ref.
NUM_HOMVAR_HOMVAR_HET	The number of sites at which both parents are homozygous for a non-reference allele and the offspring is heterozygous.
NUM_HOMREF_HOMVAR_HOM	The number of sites at which the one parent is homozygous reference, the other homozygous variant and the offspring is homozygous.
NUM_HOM_HET_HOM	The number of sites at which one parent is homozygous, the other is heterozygous and the offspring is the alternative homozygote.
NUM_HAPLOID_DENOVO	The number of sites at which the offspring is haploid, the parent is homozygous reference and the offspring is non-reference.
NUM_HAPLOID_OTHER	The number of sites at which the offspring is haploid and exhibits a reference allele that is not present in the parent.
NUM_OTHER	The number of otherwise unclassified events.
TOTAL_MENDELIAN_VIOLATIONS	The total of all mendelian violations observed.

GATK version 4.6.0.0 built at Sat, 29 Jun 2024 20:47:29 -0400.